ArticleGenome research2008
Using ChIP-chip technology to reveal common principles of transcriptional repression in normal and cancer cells.
Article in Genome research, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
33 citing papers in PubMed, 75 citations in OpenAlex.
- Dissecting myogenin-mediated retinoid X receptor signaling in myogenic differentiation.Communications biology · 2020Article
- Genome-wide DNA methylation profiles in Tibetan and Yorkshire pigs under high-altitude hypoxia.Journal of animal science and biotechnology · 2019Article
- Chemical Proteomics Identifies Druggable Vulnerabilities in a Genetically Defined Cancer.Cell · 2017Article
- Axitinib blocks Wnt/β-catenin signaling and directs asymmetric cell division in cancer.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- HDAC Inhibition Induces MicroRNA-182, which Targets RAD51 and Impairs HR Repair to Sensitize Cells to Sapacitabine in Acute Myelogenous Leukemia.Clinical cancer research : an official journal of the American Association for Cancer Research · 2016Article
- Formaldehyde crosslinking: a tool for the study of chromatin complexes.The Journal of biological chemistry · 2015Review
- The SMARCA2/4 ATPase Domain Surpasses the Bromodomain as a Drug Target in SWI/SNF-Mutant Cancers: Insights from cDNA Rescue and PFI-3 Inhibitor Studies.Cancer research · 2015Article
- Global loss of DNA methylation uncovers intronic enhancers in genes showing expression changes.Genome biology · 2014Article
- Article
- The osteoblast to osteocyte transition: epigenetic changes and response to the vitamin D3 hormone.Molecular endocrinology (Baltimore, Md.) · 2014Article
- DNA methylation temporal profiling following peripheral versus central nervous system axotomy.Scientific data · 2014Article
- Genome-wide methylation analysis of prostate tissues reveals global methylation patterns of prostate cancer.The American journal of pathology · 2013Article
- Histone deacetylases mediate the silencing of miR-15a, miR-16, and miR-29b in chronic lymphocytic leukemia.Blood · 2012Article
- Intragenic DNA methylation: implications of this epigenetic mechanism for cancer research.British journal of cancer · 2012Review
- Article
- Genome-wide principles of gene regulation by the vitamin D receptor and its activating ligand.Molecular and cellular endocrinology · 2011Review
- Temporal uncoupling of the DNA methylome and transcriptional repression during embryogenesis.Genome research · 2011Article
- Genome-wide analysis reveals PADI4 cooperates with Elk-1 to activate c-Fos expression in breast cancer cells.PLoS genetics · 2011Article
- Open chromatin in pluripotency and reprogramming.Nature reviews. Molecular cell biology · 2011Review
- Inference of hierarchical regulatory network of estrogen-dependent breast cancer through ChIP-based data.BMC systems biology · 2010Article
Corrections and comments
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Authors and funding
8 authors at 1 institution in 1 country.
Funding
Abstract
We compared 12 different cell populations, including embryonic stem cells before and during differentiation into embryoid bodies as well as various types of normal and tumor cells to determine if pluripotent versus differentiated cell types use different mechanisms to establish their transcriptome. We first identified genes that were not expressed in the 12 different cell populations and then determined which of them were regulated by histone methylation, DNA methylation, at the step of productive elongation, or by the inability to establish a preinitiation complex. For these experiments, we performed chromatin immunoprecipitation using antibodies to H3me3K27, H3me3K9, 5-methyl-cytosine, and POLR2A. We found that (1) the percentage of low expressed genes bound by POLR2A, H3me3K27, H3me3K9, or 5-methyl-cytosine is similar in all 12 cell types, regardless of differentiation or neoplastic state; (2) a gene is generally repressed by only one mechanism; and (3) distinct classes of genes are repressed by certain mechanisms. We further characterized two transitioning cell populations, 3T3 cells progressing from G0/G1 into S phase and mES cells differentiating into embryoid bodies. We found that the transient regulation through the cell cycle was achieved predominantly by changes in the recruitment of the general transcriptional machinery or by post-POLR2A recruitment mechanisms. In contrast, changes in chromatin silencing were critical for the permanent changes in gene expression in cells undergoing differentiation.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.